Residue Interactions Affecting The Deprotonation of Internal Guanine Moieties In Oligodeoxyribonucleotides, Calculated By FMO Methods

The effect of vicinal molecular groups on the intrinsic acidity of a central guanine residue in short single-stranded DNA models, and the potentials exerted by the backbone and the nucleobases on the leaving proton were determined by the Fragment Molecular Orbital (FMO) method, in terms of quantum descriptors (QD) and pair interaction interfragment decomposition analysis (PIEDA). The acidity of the central guanine moiety decreased with increasing oligonucleotide length, in response to changes by less than1 eV in the ionization potential, global softness, electrophilicity index and electronegativity descriptors. The differences in these descriptors were majorly interpreted in terms of the electrostatic influence of the negative charges residing on the backbone of the molecule. Additionally, this electric-field effect was determined explicitly for the displacement of the test hydronium ion to a distance of 250 Å from its original position, resulting in good agreement with calculations of the variation in Gibbs free energies, obtained from physical experiments conducted on the identical oligonucleotide sequences. The reported results are useful for biophysical applications of deoxyriboligonucleotides containing guanine residues in order to induce local negative charges at specific positions in the DNA chain.

Predictive models for the phase behaviour and solution properties of weak electrolytes: nitric, sulphuric, and carbonic acids

The distribution of ionic species in electrolyte systems is important in many fields of science and engineering, ranging from the study of degradation mechanisms to the design of systems for electrochemical energy storage. Often, other phenomena closely related to ionic speciation, such as ion pairing, clustering and hydrogen bonding, which are difficult to investigate experimentally, are also of interest. Here, we develop an accurate molecular approach, accounting for reactions as well as association and ion pairing, to deliver a predictive framework that helps validate experiment and guides future modelling of speciation phenomena of weak electrolytes. We extend the SAFT-VRE Mie equation of state [D. K. Eriksen et al., Mol. Phys., 2016, 114, 2724–2749] to study aqueous solutions of nitric, sulphuric, and carbonic acids, considering complete and partially dissociated models. In order to incorporate the dissociation equilibria, correlations to experimental data for the relevant thermodynamic equilibrium constants of the dissociation reactions are taken from the literature and are imposed as a boundary condition in the calculations. The models for water, the hydronium ion, and carbon dioxide are treated as transferable and are taken from our previous work. We present new molecular models for nitric acid, and the nitrate, bisulfate, sulfate, and bicarbonate anions. The resulting framework is used to predict a range of phase behaviour and solution properties of the aqueous acids over wide ranges of concentration and temperature, including the degree of dissociation, as well as the activity coefficients of the ionic species, and the activity of water and osmotic coefficient, density, and vapour pressure of the solutions. The SAFT-VRE Mie models obtained in this manner provide a means of elucidating the mechanisms of association and ion pairing in the systems studied, complementing the experimental observations reported in the literature.

Theoretical insights on the encapsulated hydronium ion mediated supramolecular assembly of nickel(II) Schiff base complexes: Strong hydrogen bonded interaction due to charge transfer from the lone pair of oxygen to the antibonding orbital of the O-H bond

To understand the packing in a particular crystal we need to investigate the supramolecular interactions. Here we report a hydronium ion encapsulated within a dimeric assembly of two different nickel(II)...

Proton transfer in bulk water using the full adaptive QM/MM method: integration of solute- and solvent-adaptive approaches

The full adaptive approach achieved an accurate and stable molecular dynamics simulation of hydronium ion in bulk.

Hydronium Ion Diffusion in Model Proton Exchange Membranes at Low Hydration: Insights from Ab Initio Molecular Dynamics

Fuel-cell deployable proton exchange membranes (PEMs) are considered to be a promising technology for clean and efficient power generation. However, a fundamental atomistic understanding of the hydronium diffusion process in...